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The problem here looks like you are trying to use portamento on arps. Portamento is best used to slide between notes with no arppegios or vibrato. I got it to sound in-tune just by removing all the 3-20 commands in your 2nd square channel.
Also in your envelopes you could save yourself some trouble by knowing that the last number is always automatically repeated. 2 2 2 2 2 | 2 2 2 is the same as 2. 9 5 3 1 1 1 1 1 1 1 is the same as 9 5 3 1.
lol, you spelled problem wrong. I noticed this with my DK Item pickup song when I played it in NotSoFatso, the notes didn't end when they were supposed to in Famitracker and I was annoyed.